@article{4ebc12e19c4a4a2cb363c78ada4c8887,
title = "Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes",
abstract = "The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present a plastid genome sequence from a nonphotosynthetic chrysophyte, “Spumella” sp. NIES-1846, and show that it has retained a nearly identical set of plastid-encoded functions as apicomplexan parasites. Our transcriptomic analysis of 12 different photosynthetic and nonphotosynthetic chrysophyte lineages reveals remarkable convergence in the functions of these nonphotosynthetic plastids, along with informative lineage-specific retentions and losses. At one extreme, Cornospumella fuschlensis retains many photosynthesis-associated proteins, although it appears to have lost the reductive pentose phosphate pathway and most plastid amino acid metabolism pathways. At the other extreme, Paraphysomonas lacks plastid-targeted proteins associated with gene expression and all metabolic pathways that require plastid-encoded partners, indicating a complete loss of plastid DNA in this genus. Intriguingly, some of the nucleus-encoded proteins that once functioned in the expression of the Paraphysomonas plastid genome have been retained. These proteins were likely to have been dual targeted to the plastid and mitochondria of the chrysophyte ancestor, and are uniquely targeted to the mitochondria in Paraphysomonas. Our comparative analyses provide insights into the process of functional reduction in nonphotosynthetic plastids.",
keywords = "Dual targeting, Heterotrophy, Ochrophyte, Phylogenomics, Protist",
author = "Dorrell, {Richard G.} and Tomonori Azuma and Mami Nomura and {de Kerdrel}, {Guillemette Audren} and Lucas Paoli and Shanshan Yang and Chris Bowler and Ishii, {Ken ichiro} and Hideaki Miyashita and Gillian Gile and Ryoma Kamikawa",
note = "Funding Information: We thank the OKED Genomics Core at Arizona State University for assistance with next-generation sequencing, Catherine Cantrel (CNRS and {\'E}cole Normale Sup{\'e}rieure) for assistance with diatom transformations, and Louis Graf (Sungkyunkwan University) for assistance with phylogenetic analyses. We thank Virginia Armbrust (University of Washington), Jackie Collier (Stony Brook University), and Connie Lovejoy (Universit{\'e} Laval), respectively, for the advance provision of genome sequence data from Pseudo-nitzschia multiseries, four species of Arctic microalgae (CCMP2298, CCMP2097, CCMP2436, and CCMP2293), and three species of marine labyrinthu-lomycetes (Aplanochytrium kerguelensis, Aurantiochytrium limnaticum, and Schizochytrium aggegatum), used to enrich the phylogenetic reference datasets used in this study. These sequence data were produced by the US Department of Energy Joint Genome Institute (https://www.jgi.doe.gov/), a Department of Energy Office of Science User Facility, supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231, in collaboration with the user community. This work was supported by a Grant-in-Aid for Young Scientists (A) from the Japan Society for the Promotion of Sciences (JSPS) (15H05606; awarded to R.K.); a JSPS Research Fellowship for Young Scientist (18J00886; awarded to M.N.); an EMBO Early Career Fellowship (Fellowship 1124/2014) and CNRS Momentum Fellowship (2018 competition) (both awarded to R.G.D.); and funding from the French Government “Investisse-ments d{\textquoteright}Avenir” Programmes MEMO LIFE Grant ANR-10-LABX-54, Universit{\'e} de Recherche Paris Sciences et Lettres (PSL) Grant ANR-1253 11-IDEX-0001-02, and OCEANOMICS Grant ANR-11-BTBR-0008 (awarded to C.B.). Funding Information: ACKNOWLEDGMENTS. We thank the OKED Genomics Core at Arizona State University for assistance with next-generation sequencing, Catherine Cantrel (CNRS and {\'E}cole Normale Sup{\'e}rieure) for assistance with diatom transformations, and Louis Graf (Sungkyunkwan University) for assistance with phylogenetic analyses. We thank Virginia Armbrust (University of Washington), Jackie Collier (Stony Brook University), and Connie Lovejoy (Universit{\'e} Laval), respectively, for the advance provision of genome sequence data from Pseudo-nitzschia multiseries, four species of Arctic microalgae (CCMP2298, CCMP2097, CCMP2436, and CCMP2293), and three species of marine labyrinthu-lomycetes (Aplanochytrium kerguelensis, Aurantiochytrium limnaticum, and Schizochytrium aggegatum), used to enrich the phylogenetic reference datasets used in this study. These sequence data were produced by the US Department of Energy Joint Genome Institute (https://www.jgi.doe.gov/), a Department of Energy Office of Science User Facility, supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231, in collaboration with the user community. This work was supported by a Grant-in-Aid for Young Scientists (A) from the Japan Society for the Promotion of Sciences (JSPS) (15H05606; awarded to R.K.); a JSPS Research Fellowship for Young Scientist (18J00886; awarded to M.N.); an EMBO Early Career Fellowship (Fellowship 1124/2014) and CNRS Momentum Fellowship (2018 competition) (both awarded to R.G.D.); and funding from the French Government “Investisse-ments d{\textquoteright}Avenir” Programmes MEMO LIFE Grant ANR-10-LABX-54, Universit{\'e} de Recherche Paris Sciences et Lettres (PSL) Grant ANR-1253 11-IDEX-0001-02, and OCEANOMICS Grant ANR-11-BTBR-0008 (awarded to C.B.). Publisher Copyright: {\textcopyright} 2019 National Academy of Sciences. All Rights Reserved.",
year = "2019",
month = apr,
day = "2",
doi = "10.1073/pnas.1819976116",
language = "English (US)",
volume = "116",
pages = "6914--6923",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
publisher = "National Academy of Sciences",
number = "14",
}